Measurement of refractive index-profile of the optical fiber preforms is important for controlling the quality of optical fiber waveguides and also for specification of additional treatment (overcoating or etching) of the preform before drawing the fiber. For preforms, non-destructive techniques are particularly useful. Some of the techniques are based on measurement of the deflection of a transversely directed light beam scanned along the diameter of the preform. This technique is implemented in various commercially available instruments but the refractive index profile is mostly calculated with the assumption that the preform is circular. In the contribution we present method that we developed for tomography reconstruction of refractive index profile and outer geometry of preforms with highly asymmetric cross section. The method is based on numerical processing of a set of measured deflection functions at many angular projections. Practical aspects of processing the measured set of deflection functions will be discussed in detail on two examples: cylindrical preform with highly elliptical gradient-index core for optical fiber for evanescent-wave sensing and non-cylindrical preform with stadium-like cross section for cladding-pumped fiber lasers.